Advances in technology over the last decade have resulted in a golden age of genomics in life sciences. Sequencing technology has yielded 169 completed and published genomes, including human, and there are 432 prokaryotic and 367 eukaryotic genome-sequencing projects ongoing. This explosion in sequence information has been coupled with the development of many high throughput technologies, such as microarrays, which have given us an unprecedented capacity to assay almost every aspect of genomes and the biological systems they direct. A critical gap in our framework for comprehensive understanding of biological systems is that despite having finished genome sequences for 21 eukaryotes, there is probably no single eukaryote for which we can say with confidence that we have a full list of all the genes and their products. The budding yeast, Saccharomyces cerevisiae, was the first eukaryotic genome to be fully sequenced, and is arguably the pre-eminent organism for genomic studies, and many key eukaryotic pathways and mechanisms have been elucidated in yeast. In the eight years since S. cerevisiae was sequenced, numerous studies have resulted in the addition or removal of genes from the Saccharomyces Genome Database, yet hundreds of ambiguities remain. This application seeks to use a novel iterative custom microarray approach to comprehensively define the genic potential of the yeast genome, by identifying and sizing all transcripts within the genome, and determining whether they are protein coding or not. Initial characterization of novel transcripts, to define their functions, will be carried out. Preliminary tudies suggest that there is a wealth of undiscovered genes in yeast, and that this study will form a prototypic methodology for rapidly determining the transcriptomes of a wide variety of organisms, and for providing an interpretive framework for initial functional characterization of these transcriptomes.